When we say intake it's the filter and pipe up to the throttle body, when someone is talking about the intake manifold it will be refered to most commonly as the intake mani. first lets clear up what you think a cold air intake (cai) is. what you probably see on most cars is a short ram intake. it's si8mply a tube with a filter and it sits at approx the same height as the stock air filter, the cai actually locates the filter lower in the engine bay or behind the bumper but it is considerably lower to the ground. given this is florida and rain is a bitch the cai will easily be submersed in puddles that you will come across every day ( in rainy season). so the car will suck up water and the engine gets fucked. the aem bypass is good in theory and actually does work....to a degree, also if the bypass doesn't full work, I.E. you still suck up a little water then your motor is still screwed and aem will only replace the malfunctioning part not you new motor shaped paper weight. so the best idea is to just get one that puts the filter at approx the same height as the oem filter or higher.

the whole exhaust system form the header all the way to tail pipe would need replacement. depending on what area your in and how strict they are with emmission control fuck the cat, pull it, put in a "resonator" ( a pipe with a slight bulge ) then run a 2.25" exhaust all the way to your performance muffler.

an intake mani can run a few hundred dollars and while it along with the throttle body upgrade and port matching are a good idea, you won't see alot of gain in hp until you run forced induction(fi) or naturally asperated (na) at high hp.

an upgraded clutch is a good idea, but if yours is still pretty new you can afford to wait. Until you get over 200hp on the d-series engine the stock clutch will hold, however if you are in need of a new clutch, or are replacing the flywheel ( a very good idea) then a simple stock upgrade like the exedy clutch I believe stage 1. the stage 1 gives a little more holding power over stock but doesn't break you wallet.

the flywheel, definately a must do on the under torqued honda motor, any lighter than 9lbs and it is too light and will actually hinder your performance. get one that is made that light and not a stock regrind.

unless this is a track only car, keep the a/c. I repeat keep the a/c, it's florida and the extra 1/4hp and .01 second off your 1/4 are not worth spending 5 days to and from work in the fl heat.

Underdrive pulleys are also a decent upgrade, just make sure you have a big socket, a really big pry bar and a couple friends. ( the main bolt can be a bitch.)